The Y-chromosome point mutation rate in humans

Area of Science:

• Genetics
• Evolutionary Biology
• Genomics

Background:

• Mutations are essential for biological variation and are critical parameters in evolutionary and medical research.
• Estimating mutation rates aids in understanding evolutionary processes and genetic disease.
• The male-specific Y chromosome (MSY) offers a unique region for studying mutation rates due to its unique inheritance pattern.

Purpose of the Study:

• To estimate the de novo mutation rate across different regions of the male-specific Y chromosome (MSY).
• To compare mutation rates between palindromic (PAL) and non-palindromic regions of the MSY.
• To investigate potential differences in mutation rates that may indicate DNA repair mechanisms.

Main Methods:

• Whole-genome sequencing data from 753 Icelandic males across 274 patrilines were analyzed.
• Mutation rates were calculated based on 1,365 meioses, covering approximately 47,123 years.
• Specific regions of the MSY, including XDG, XTR, rAMP, and PAL sequences, were assessed.

Main Results:

• The combined mutation rate for XDG, XTR, and rAMP sequences was 8.71 × 10⁻¹⁰ mutations per position per year (PPPY).
• A significantly lower mutation rate of 7.37 × 10⁻¹⁰ PPPY was observed in palindromic (PAL) regions of the MSY.
• The mutation rate in PAL regions was comparable to that of paternally transmitted autosomes (7.2 × 10⁻¹⁰ PPPY).

Conclusions:

• The male-specific Y chromosome (MSY) exhibits varying mutation rates across its different sequence types.
• Palindromic (PAL) regions of the MSY show a reduced mutation rate compared to other MSY regions.
• This rate difference in PAL regions may reflect the efficacy of gene conversion in repairing de novo mutations.